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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-06-04, 01:44 based on data in: /media/vincent/Data/panax/2_trimmed/pooled_sample/fastQC


        General Statistics

        Showing 329/329 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        fastQC | 1
        76.7%
        52%
        1.9
        fastQC | 10
        88.7%
        46%
        4.7
        fastQC | 100
        85.9%
        48%
        5.2
        fastQC | 101
        88.9%
        50%
        9.1
        fastQC | 102
        88.7%
        45%
        5.7
        fastQC | 103
        89.4%
        48%
        10.1
        fastQC | 104
        88.5%
        44%
        7.9
        fastQC | 105
        57.5%
        48%
        1.3
        fastQC | 106
        58.1%
        49%
        1.1
        fastQC | 107
        60.2%
        49%
        1.2
        fastQC | 108
        88.2%
        51%
        10.6
        fastQC | 109
        84.8%
        58%
        1.4
        fastQC | 11
        81.7%
        42%
        1.4
        fastQC | 110
        59.5%
        51%
        1.1
        fastQC | 111
        56.2%
        53%
        1.5
        fastQC | 112
        57.8%
        51%
        2.0
        fastQC | 113
        86.5%
        45%
        6.2
        fastQC | 114
        89.3%
        48%
        15.9
        fastQC | 115
        86.1%
        48%
        7.6
        fastQC | 116
        86.8%
        48%
        11.9
        fastQC | 117
        86.2%
        47%
        5.4
        fastQC | 118
        86.5%
        46%
        8.3
        fastQC | 119
        91.5%
        45%
        20.3
        fastQC | 12
        84.7%
        41%
        2.0
        fastQC | 120
        86.6%
        48%
        13.9
        fastQC | 121
        65.8%
        41%
        1.8
        fastQC | 122
        61.5%
        42%
        1.3
        fastQC | 123
        87.8%
        58%
        3.8
        fastQC | 124
        88.0%
        57%
        3.4
        fastQC | 125
        60.9%
        56%
        1.3
        fastQC | 126
        89.7%
        57%
        6.9
        fastQC | 127
        88.6%
        57%
        5.6
        fastQC | 128
        87.9%
        57%
        3.9
        fastQC | 129
        88.8%
        48%
        4.3
        fastQC | 13
        90.8%
        41%
        5.9
        fastQC | 130
        86.7%
        58%
        5.2
        fastQC | 131
        60.6%
        46%
        1.0
        fastQC | 132
        88.6%
        49%
        3.2
        fastQC | 133
        89.3%
        50%
        3.4
        fastQC | 134
        89.1%
        55%
        3.9
        fastQC | 135
        89.2%
        50%
        3.9
        fastQC | 136
        87.7%
        52%
        2.7
        fastQC | 137
        59.9%
        48%
        0.8
        fastQC | 138
        87.9%
        52%
        3.0
        fastQC | 139
        76.4%
        49%
        3.0
        fastQC | 14
        67.0%
        42%
        1.4
        fastQC | 140
        75.5%
        50%
        2.5
        fastQC | 141
        75.8%
        49%
        2.5
        fastQC | 142
        76.2%
        50%
        2.7
        fastQC | 143
        80.3%
        46%
        2.4
        fastQC | 144
        76.1%
        49%
        2.2
        fastQC | 145
        77.4%
        49%
        4.3
        fastQC | 146
        76.3%
        52%
        3.1
        fastQC | 147
        87.1%
        56%
        2.5
        fastQC | 148
        86.7%
        55%
        2.8
        fastQC | 149
        85.5%
        55%
        2.0
        fastQC | 15
        88.1%
        47%
        2.9
        fastQC | 150
        87.0%
        53%
        2.6
        fastQC | 151
        90.3%
        55%
        1.3
        fastQC | 152
        86.6%
        52%
        2.6
        fastQC | 153
        88.5%
        53%
        4.3
        fastQC | 154
        68.5%
        58%
        1.0
        fastQC | 155
        87.9%
        47%
        2.9
        fastQC | 156
        85.1%
        55%
        2.1
        fastQC | 157
        88.3%
        46%
        3.0
        fastQC | 158
        88.4%
        44%
        2.8
        fastQC | 159
        88.1%
        47%
        3.0
        fastQC | 16
        89.6%
        43%
        3.8
        fastQC | 160
        92.8%
        45%
        2.6
        fastQC | 161
        88.4%
        48%
        3.0
        fastQC | 162
        92.9%
        44%
        2.1
        fastQC | 163
        89.8%
        46%
        7.0
        fastQC | 164
        88.0%
        46%
        5.3
        fastQC | 165
        88.0%
        47%
        5.8
        fastQC | 166
        92.1%
        47%
        19.3
        fastQC | 167
        90.1%
        46%
        6.1
        fastQC | 168
        89.0%
        48%
        6.0
        fastQC | 169
        89.9%
        45%
        5.9
        fastQC | 17
        88.3%
        59%
        4.1
        fastQC | 170
        89.6%
        46%
        5.8
        fastQC | 171
        80.0%
        48%
        1.8
        fastQC | 172
        87.2%
        46%
        5.4
        fastQC | 173
        89.8%
        45%
        4.1
        fastQC | 174
        86.8%
        50%
        6.3
        fastQC | 175
        89.0%
        44%
        3.4
        fastQC | 176
        88.8%
        42%
        5.0
        fastQC | 177
        86.0%
        47%
        3.7
        fastQC | 178
        78.0%
        43%
        2.3
        fastQC | 179
        83.8%
        55%
        2.1
        fastQC | 18
        88.7%
        55%
        8.2
        fastQC | 180
        83.8%
        53%
        2.3
        fastQC | 181
        83.6%
        51%
        2.1
        fastQC | 182
        89.0%
        50%
        3.3
        fastQC | 183
        85.4%
        56%
        2.1
        fastQC | 184
        83.7%
        54%
        2.1
        fastQC | 185
        88.0%
        52%
        2.9
        fastQC | 186
        84.7%
        53%
        3.3
        fastQC | 187
        89.6%
        47%
        1.9
        fastQC | 188
        86.4%
        47%
        2.0
        fastQC | 189
        86.4%
        49%
        2.0
        fastQC | 19
        87.6%
        57%
        5.4
        fastQC | 190
        86.2%
        47%
        2.2
        fastQC | 191
        87.0%
        46%
        2.7
        fastQC | 192
        88.2%
        45%
        1.2
        fastQC | 193
        90.0%
        46%
        1.9
        fastQC | 194
        84.7%
        48%
        1.8
        fastQC | 195
        87.0%
        45%
        2.3
        fastQC | 196
        89.1%
        45%
        3.5
        fastQC | 197
        88.8%
        47%
        3.3
        fastQC | 198
        88.7%
        46%
        4.1
        fastQC | 199
        88.6%
        46%
        3.9
        fastQC | 2
        79.4%
        56%
        0.7
        fastQC | 20
        88.6%
        49%
        7.1
        fastQC | 200
        90.0%
        43%
        3.8
        fastQC | 201
        84.8%
        48%
        2.8
        fastQC | 202
        89.0%
        45%
        3.2
        fastQC | 203
        86.9%
        50%
        2.5
        fastQC | 204
        91.2%
        51%
        1.7
        fastQC | 205
        91.8%
        49%
        1.5
        fastQC | 206
        89.1%
        49%
        3.2
        fastQC | 207
        92.9%
        47%
        2.0
        fastQC | 208
        89.2%
        53%
        3.8
        fastQC | 209
        90.5%
        49%
        1.2
        fastQC | 21
        88.2%
        58%
        5.7
        fastQC | 210
        92.9%
        50%
        2.3
        fastQC | 211
        89.8%
        49%
        3.7
        fastQC | 212
        71.9%
        52%
        1.4
        fastQC | 213
        87.1%
        53%
        2.4
        fastQC | 214
        74.0%
        49%
        1.6
        fastQC | 215
        89.8%
        49%
        4.8
        fastQC | 216
        71.3%
        50%
        1.3
        fastQC | 217
        90.7%
        50%
        7.5
        fastQC | 218
        90.0%
        51%
        5.4
        fastQC | 219
        87.6%
        44%
        5.7
        fastQC | 22
        88.8%
        56%
        8.7
        fastQC | 220
        86.7%
        45%
        5.1
        fastQC | 221
        88.7%
        44%
        3.4
        fastQC | 222
        88.3%
        45%
        4.5
        fastQC | 223
        87.2%
        44%
        5.6
        fastQC | 224
        87.5%
        44%
        5.7
        fastQC | 225
        75.4%
        44%
        2.6
        fastQC | 226
        86.2%
        47%
        5.7
        fastQC | 227
        87.9%
        52%
        3.5
        fastQC | 228
        84.3%
        53%
        1.9
        fastQC | 229
        86.5%
        52%
        2.7
        fastQC | 23
        88.7%
        56%
        5.0
        fastQC | 230
        87.0%
        51%
        2.8
        fastQC | 231
        91.0%
        54%
        1.3
        fastQC | 232
        86.4%
        51%
        2.3
        fastQC | 233
        86.6%
        54%
        3.2
        fastQC | 234
        90.2%
        55%
        1.5
        fastQC | 235
        88.1%
        56%
        4.5
        fastQC | 236
        88.1%
        54%
        3.5
        fastQC | 237
        87.5%
        57%
        3.2
        fastQC | 238
        71.4%
        53%
        2.1
        fastQC | 239
        90.4%
        55%
        2.5
        fastQC | 24
        89.0%
        55%
        10.3
        fastQC | 241
        89.1%
        52%
        4.9
        fastQC | 242
        70.3%
        50%
        1.3
        fastQC | 243
        89.1%
        47%
        4.0
        fastQC | 244
        88.2%
        46%
        3.0
        fastQC | 245
        88.4%
        49%
        3.5
        fastQC | 246
        90.0%
        48%
        8.5
        fastQC | 247
        85.0%
        47%
        3.4
        fastQC | 248
        89.3%
        46%
        3.5
        fastQC | 249
        87.5%
        49%
        2.7
        fastQC | 25
        66.0%
        42%
        1.8
        fastQC | 250
        88.1%
        47%
        2.8
        fastQC | 251
        87.1%
        46%
        1.5
        fastQC | 252
        85.9%
        47%
        1.6
        fastQC | 253
        83.7%
        43%
        1.9
        fastQC | 254
        86.6%
        47%
        3.1
        fastQC | 255
        86.5%
        47%
        1.2
        fastQC | 256
        85.1%
        47%
        2.1
        fastQC | 257
        83.3%
        47%
        1.6
        fastQC | 258
        90.4%
        47%
        1.2
        fastQC | 259
        88.2%
        54%
        2.4
        fastQC | 26
        69.5%
        40%
        1.6
        fastQC | 260
        88.1%
        53%
        2.5
        fastQC | 261
        85.4%
        53%
        2.1
        fastQC | 262
        88.3%
        52%
        3.0
        fastQC | 263
        93.0%
        54%
        2.2
        fastQC | 264
        86.0%
        54%
        2.1
        fastQC | 265
        93.1%
        53%
        2.5
        fastQC | 266
        91.1%
        49%
        2.8
        fastQC | 267
        90.6%
        47%
        1.3
        fastQC | 268
        86.9%
        48%
        1.4
        fastQC | 269
        88.1%
        44%
        1.9
        fastQC | 27
        71.5%
        43%
        1.7
        fastQC | 270
        88.4%
        45%
        2.6
        fastQC | 271
        68.1%
        47%
        0.8
        fastQC | 272
        87.1%
        44%
        1.8
        fastQC | 273
        87.1%
        44%
        1.6
        fastQC | 274
        88.9%
        43%
        1.6
        fastQC | 275
        87.9%
        52%
        1.5
        fastQC | 276
        86.1%
        55%
        1.5
        fastQC | 277
        86.0%
        57%
        2.6
        fastQC | 278
        85.2%
        56%
        2.1
        fastQC | 279
        90.2%
        52%
        1.0
        fastQC | 28
        68.1%
        41%
        1.8
        fastQC | 280
        82.3%
        51%
        2.4
        fastQC | 281
        88.3%
        54%
        1.2
        fastQC | 282
        86.7%
        56%
        1.5
        fastQC | 283
        88.2%
        58%
        3.9
        fastQC | 284
        84.2%
        59%
        5.9
        fastQC | 285
        86.2%
        52%
        2.5
        fastQC | 286
        88.7%
        46%
        3.0
        fastQC | 287
        88.9%
        63%
        4.5
        fastQC | 288
        69.9%
        58%
        1.6
        fastQC | 289
        89.2%
        55%
        4.4
        fastQC | 29
        64.7%
        43%
        1.9
        fastQC | 290
        91.8%
        53%
        2.5
        fastQC | 291
        84.6%
        49%
        7.6
        fastQC | 292
        87.1%
        45%
        4.7
        fastQC | 293
        86.3%
        46%
        4.5
        fastQC | 294
        76.7%
        46%
        5.1
        fastQC | 295
        87.9%
        42%
        4.6
        fastQC | 296
        87.9%
        43%
        4.5
        fastQC | 297
        86.4%
        47%
        4.3
        fastQC | 298
        87.5%
        45%
        6.1
        fastQC | 299
        88.4%
        51%
        3.1
        fastQC | 3
        75.0%
        56%
        1.2
        fastQC | 30
        69.3%
        40%
        1.6
        fastQC | 300
        88.0%
        50%
        2.2
        fastQC | 301
        89.2%
        54%
        6.4
        fastQC | 302
        91.4%
        49%
        4.9
        fastQC | 303
        87.7%
        49%
        2.8
        fastQC | 304
        90.1%
        50%
        3.8
        fastQC | 305
        89.1%
        49%
        3.9
        fastQC | 306
        90.1%
        56%
        5.6
        fastQC | 307
        88.1%
        46%
        3.3
        fastQC | 308
        87.5%
        48%
        2.8
        fastQC | 309
        87.3%
        47%
        2.7
        fastQC | 31
        64.6%
        43%
        1.7
        fastQC | 310
        88.9%
        44%
        3.4
        fastQC | 311
        88.9%
        46%
        3.5
        fastQC | 312
        89.2%
        43%
        3.1
        fastQC | 313
        88.7%
        45%
        3.6
        fastQC | 314
        87.1%
        49%
        2.6
        fastQC | 315
        87.4%
        50%
        3.1
        fastQC | 316
        84.7%
        48%
        2.9
        fastQC | 317
        84.8%
        50%
        2.9
        fastQC | 318
        85.4%
        49%
        2.6
        fastQC | 319
        84.7%
        47%
        3.5
        fastQC | 32
        67.3%
        40%
        1.5
        fastQC | 320
        86.5%
        48%
        3.5
        fastQC | 321
        87.9%
        49%
        3.0
        fastQC | 322
        84.8%
        50%
        2.3
        fastQC | 323
        89.3%
        46%
        4.3
        fastQC | 324
        88.2%
        47%
        4.2
        fastQC | 325
        89.0%
        50%
        4.3
        fastQC | 326
        89.2%
        49%
        5.2
        fastQC | 327
        89.5%
        47%
        5.0
        fastQC | 328
        89.4%
        46%
        4.2
        fastQC | 329
        89.3%
        47%
        4.3
        fastQC | 33
        90.9%
        43%
        6.7
        fastQC | 330
        89.5%
        44%
        3.2
        fastQC | 34
        82.7%
        43%
        1.5
        fastQC | 35
        63.2%
        49%
        1.7
        fastQC | 36
        88.2%
        45%
        2.6
        fastQC | 37
        90.7%
        47%
        6.8
        fastQC | 38
        68.6%
        42%
        1.9
        fastQC | 39
        86.2%
        43%
        1.1
        fastQC | 4
        81.9%
        49%
        1.0
        fastQC | 40
        83.9%
        42%
        1.9
        fastQC | 41
        89.4%
        46%
        4.1
        fastQC | 42
        87.1%
        50%
        2.2
        fastQC | 43
        85.6%
        51%
        1.9
        fastQC | 44
        88.1%
        54%
        3.1
        fastQC | 45
        89.2%
        49%
        3.9
        fastQC | 46
        86.2%
        59%
        0.8
        fastQC | 47
        88.0%
        49%
        2.5
        fastQC | 48
        87.7%
        49%
        2.7
        fastQC | 49
        87.8%
        43%
        5.5
        fastQC | 5
        74.0%
        57%
        1.5
        fastQC | 50
        87.2%
        44%
        4.9
        fastQC | 51
        88.0%
        45%
        6.1
        fastQC | 52
        90.5%
        44%
        14.1
        fastQC | 53
        86.2%
        47%
        3.2
        fastQC | 54
        87.4%
        48%
        6.1
        fastQC | 55
        89.2%
        47%
        12.7
        fastQC | 56
        87.5%
        42%
        3.8
        fastQC | 57
        89.3%
        49%
        5.9
        fastQC | 58
        89.2%
        48%
        4.3
        fastQC | 59
        89.0%
        47%
        3.6
        fastQC | 6
        79.2%
        47%
        2.9
        fastQC | 60
        61.6%
        47%
        1.3
        fastQC | 61
        57.0%
        52%
        1.9
        fastQC | 62
        86.9%
        48%
        2.4
        fastQC | 63
        87.9%
        49%
        4.9
        fastQC | 64
        86.7%
        46%
        1.0
        fastQC | 65
        81.9%
        41%
        1.5
        fastQC | 66
        68.1%
        41%
        1.7
        fastQC | 67
        90.1%
        43%
        5.1
        fastQC | 68
        84.6%
        42%
        2.6
        fastQC | 69
        90.4%
        41%
        4.6
        fastQC | 7
        76.2%
        55%
        1.9
        fastQC | 70
        90.7%
        40%
        5.4
        fastQC | 71
        65.9%
        42%
        1.4
        fastQC | 72
        83.2%
        43%
        1.0
        fastQC | 73
        88.9%
        46%
        12.6
        fastQC | 74
        89.2%
        44%
        10.2
        fastQC | 75
        87.2%
        44%
        5.1
        fastQC | 76
        91.5%
        45%
        17.4
        fastQC | 77
        89.0%
        44%
        10.1
        fastQC | 78
        88.2%
        44%
        9.6
        fastQC | 79
        89.2%
        44%
        12.6
        fastQC | 8
        77.3%
        50%
        1.7
        fastQC | 80
        89.4%
        43%
        7.5
        fastQC | 81
        87.7%
        48%
        2.9
        fastQC | 82
        88.6%
        46%
        3.6
        fastQC | 83
        90.3%
        43%
        8.2
        fastQC | 84
        90.2%
        46%
        9.8
        fastQC | 85
        89.9%
        46%
        7.2
        fastQC | 86
        86.0%
        48%
        0.9
        fastQC | 87
        89.4%
        51%
        9.2
        fastQC | 88
        90.4%
        43%
        5.8
        fastQC | 89
        89.4%
        43%
        3.5
        fastQC | 9
        64.5%
        44%
        1.9
        fastQC | 90
        90.5%
        44%
        5.1
        fastQC | 91
        83.0%
        41%
        1.8
        fastQC | 92
        81.9%
        46%
        1.0
        fastQC | 93
        62.7%
        44%
        1.3
        fastQC | 94
        83.6%
        39%
        1.7
        fastQC | 95
        90.2%
        40%
        3.7
        fastQC | 96
        82.5%
        42%
        1.5
        fastQC | 97
        88.8%
        48%
        5.2
        fastQC | 98
        90.6%
        46%
        10.7
        fastQC | 99
        89.0%
        45%
        6.3

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        329 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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